GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacD in Burkholderia phytofirmans PsJN

Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase

Query= reanno::Smeli:SM_b20890
         (579 letters)



>FitnessBrowser__BFirm:BPHYT_RS04815
          Length = 557

 Score =  332 bits (852), Expect = 2e-95
 Identities = 211/547 (38%), Positives = 310/547 (56%), Gaps = 23/547 (4%)

Query: 27  HRSWMKNQGLPADTFDGRPIIGICNTWSELTPCNAHLRDLAERVKRGVYEAGGFPVEF-- 84
           +RS     G     FD +P+IGI N  S +TPCNA L+ LA+     +  A   P  F  
Sbjct: 19  NRSMYYALGYEKADFD-KPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGT 77

Query: 85  PVFSTGESTLRPT---AMMFRNLAAMDVEESIRGNPVDGVVLLGGCDKTTPSLLMGAASV 141
           P  S G S        +++ R + +  +E  ++G  +DGVV++GGCDK  P  ++G    
Sbjct: 78  PTISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRT 137

Query: 142 DIPAIVVSGGPMLNGKWRGKD---VGSGTAIWQFSEMVKSGEMSLEEFMDAEQGMARSAG 198
           ++P+I V GG +  G W+G D   V S  A+ +F+    +G MS E+F   EQ    S G
Sbjct: 138 NVPSIYVYGGTIRPGNWKGTDLTIVSSFEAVGEFT----AGRMSQEDFDGIEQNACPSTG 193

Query: 199 SCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLTGRRIVEMVKEDLKPSDIL 258
           SC  M TA+TM+S  EALGM+L  ++ +   D  +   +  + R +VE VK+DLKP DI+
Sbjct: 194 SCGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKKDLKPRDIV 253

Query: 259 TKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWDRLGRDVPTIVNLQPSGKY 318
           TK++ ENA+ V  A GGSTNAVLH LA+A    V+ S+DD++R+ + VP I NL+PSG++
Sbjct: 254 TKKSIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPSGQF 313

Query: 319 LMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTI---WNDVKGVVNYNEDVILPREKA 375
           +  + + AGG+P V+K + + GLLH D IT++G TI     DV G    ++ VI P ++A
Sbjct: 314 VATDLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPRADQQVIFPIDQA 373

Query: 376 LTKSGGIAVLRGNLAPRGAVLKPSAASPHLMQHKGRAVVFESIEDYHARINREDLDIDET 435
           L K G +A+L+GNLA  GAV K +     ++   G A VF+  +     I  + +   + 
Sbjct: 374 LYKEGHLAILKGNLAVDGAVAKITGLKNPVI--TGPARVFDDEQSALEAILADKIVAGD- 430

Query: 436 CIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGITDMI-RISDARMSGTAYGTVILHTAPE 494
            ++VL+Y GPKG PGM E+  +     ++ KG+ + +  I+D R SG  +G V+ H APE
Sbjct: 431 -VVVLRYLGPKGGPGMPEM--LAPTSAIIGKGLGESVGLITDGRFSGGTWGMVVGHVAPE 487

Query: 495 AAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVKPLTGGYGGLYIKTV 554
           A  GG +A V+ GD I +D     L L++ + EL RRRAAW  P    T G    Y    
Sbjct: 488 AFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAAWQQPKPRYTRGVMAKYFALA 547

Query: 555 MQADAGA 561
             A+ GA
Sbjct: 548 QPANKGA 554


Lambda     K      H
   0.318    0.135    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 932
Number of extensions: 57
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 579
Length of database: 557
Length adjustment: 36
Effective length of query: 543
Effective length of database: 521
Effective search space:   282903
Effective search space used:   282903
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory